Research Interests in the Post GroupResearch interests of the Post group include the regulation and functional aspects of protein-protein interactions, enzymatic catalysis and activation, and protein structure. Multidimensional spin magnetic resonance methods are used to determine three-dimensional structures and internal dynamics of protein complexes. Computational methods are used to understand the structural basis for protein stability, protein-ligand binding energetics, enzymatic regulation and activity, and the mechanism of action of antiviral compounds.
As a part of the Purdue Cancer Center we are determining the structures of key domains of the kinases involved in B-cell activation. In collaboration with Bob Gaehlen and Marietta Harrison, we are working to understand the binding and specificity of the Src Homolgy 2 (SH2) domains of these proteins. SH2 domains recognize phosphorylated tyrosine residues in a sequence dependent manner to aid in proper recruiting and activation of signaling proteins. Detailed knowledge of these interactions will aid in our understanding of the mechanisms behind the regulation of these pathways, which are important to cancer research.
We are developing computer protocols that incorporate structural information obtained with comparative modeling techniques of related proteins with known structure to help increase the accuracy of calculated protein structures. Methods to improve the accuracy of analyzing and predicting NMR data are also being examined in these efforts.Back to Top
Members of our group are applying computational techniques to understand the conformational changes involved in protein activation. These studies are probing the enzymatic activation of Src Kinases as well as the changes involved in the final stages of virus maturation. Biased molecular dynamics simulations are employed to model the transition from an active conformation to an inactive conformation and vice versa. Analysis of these pathways will potentially uncover key transitional events that remain unobserved and cannot be deduced from the static crystal structures of each end state alone. Deeper understanding of the events of an activation or inactivation process could aid in rational drug design efforts to target and inhibit key protein functions.Back to Top
Drug DesignMolecular dynamics and docking simulations are also being employed to understand drug binding in atomic detail. Docking simulations serve to predict the affinity of a drug for a predicted binding pocket. This allows an initial screening of large libraries of potential drug candidates, in an effort to increase the speed and efficiency of the design process. Screening is currently being conducted for the development of antiviral agents. Molecular dynamics simulations and free energy calculations are also being conducted and compared to experimental thermodynamic data in an effort to better understand the structural basis of drug binding. Biased molecular dynamics simulations are being employed to study drug dissociation events in an effort to refine currently developed drug candidates. These simulations predict likely key interactions that occur as a drug binds and dissociates from the target protein. As with the activation and inactivation of activity, the dynamics simulations have the potential to uncover transient interactions that are not likely to be deduced from static structures of the bound and unbound states. Knowledge of these dynamic interactions may indicate sites on the drug candidate for potential improvement that would not have been predicted otherwise. Back to Top
Protein StabilityMolecular dynamics simulations are also providing insight into the forces controlling protein stability. This insight is derived from comparison of simulations of mesophilic proteins with their thermophilic counterparts, undertaken to investigate the structural elements that are mutated or conserved to shift the folding free energy minimum to different temperatures. Recent results (Dadarlat V and Post CB: PNAS 2003) indicate that the charge distribution between the protein surface and core correlates to the protein compressibility across a series of mesophile/thermophile comparisons. Further detailed analysis of simulation trajectories is being conducted to further understand the interactions resulting in this correlation.
We are also interested in a deeper understanding of ligand binding thermodynamics. The size and complexity of protein systems has long frustrated attempts at fully decomposing free energy, enthalpy, and entropy measurements from calorimetric binding studies into contributions from specific interactions that are observed in static structures. New work in the group is attempting to compare free energies, entropy contributions, and dynamic order parameters calculated from molecular dynamics simulations to experimental data obtained from calorimetry and NMR, to more completely characterize important interactions and fluctuations in the complex structure that contribute to each thermodynamic property. Improved understanding of these contributions has the potential to help improve binding affinity through rational drug design.Back to Top